Starting phenix.real_space_refine on Wed Feb 21 04:29:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4p_28856/02_2024/8f4p_28856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4p_28856/02_2024/8f4p_28856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4p_28856/02_2024/8f4p_28856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4p_28856/02_2024/8f4p_28856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4p_28856/02_2024/8f4p_28856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4p_28856/02_2024/8f4p_28856.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3104 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 16951 2.51 5 N 4399 2.21 5 O 5165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26635 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8375 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 bond proxies already assigned to first conformer: 8551 Chain: "B" Number of atoms: 8524 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 bond proxies already assigned to first conformer: 8708 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 56, 'TRANS': 1010} Chain breaks: 5 Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 868 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 459 " occ=0.51 ... (10 atoms not shown) pdb=" OG BSER A 459 " occ=0.49 residue: pdb=" N ASER B 459 " occ=0.67 ... (10 atoms not shown) pdb=" OG BSER B 459 " occ=0.33 Time building chain proxies: 20.22, per 1000 atoms: 0.76 Number of scatterers: 26635 At special positions: 0 Unit cell: (163.572, 162.503, 200.991, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5165 8.00 N 4399 7.00 C 16951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 331 " " NAG A1203 " - " ASN A 603 " " NAG A1204 " - " ASN A 616 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A 717 " " NAG A1207 " - " ASN A1098 " " NAG A1208 " - " ASN A1134 " " NAG A1209 " - " ASN A 657 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 331 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C 717 " " NAG C1207 " - " ASN C1134 " " NAG C1208 " - " ASN C 343 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN B1134 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 343 " Time building additional restraints: 10.14 Conformation dependent library (CDL) restraints added in 7.6 seconds 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6248 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 47 sheets defined 22.5% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.824A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.944A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.033A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.645A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.840A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.029A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.524A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.702A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.636A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.640A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1032 removed outlier: 4.303A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.742A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.168A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.790A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.611A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.652A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.921A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.531A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.603A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.386A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.604A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.430A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.656A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.827A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.657A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.719A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.609A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.183A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 4.151A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.871A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.714A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1146' Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.737A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.818A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.701A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 156 removed outlier: 4.379A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.919A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.602A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.667A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.658A pdb=" N ILE A 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.601A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.774A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 53 removed outlier: 4.301A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 160 through 172 removed outlier: 9.225A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.546A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.560A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.542A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.752A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 643 through 645 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.007A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.688A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.474A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.545A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 53 Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.503A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 106 Processing sheet with id=AD8, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.594A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.750A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.429A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 398 through 399 removed outlier: 3.833A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.164A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.530A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.517A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.346A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 99 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP D 100 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.346A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 99 " --> pdb=" O GLY D 33 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.70 Time building geometry restraints manager: 10.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8530 1.34 - 1.47: 6924 1.47 - 1.60: 11647 1.60 - 1.73: 0 1.73 - 1.86: 152 Bond restraints: 27253 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N SER A 884 " pdb=" CA SER A 884 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.67e+00 bond pdb=" N THR B 167 " pdb=" CA THR B 167 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.17e-02 7.31e+03 6.72e+00 bond pdb=" N VAL D 101 " pdb=" CA VAL D 101 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.58e+00 bond pdb=" N ASP D 100 " pdb=" CA ASP D 100 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.31e-02 5.83e+03 6.07e+00 ... (remaining 27248 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.30: 722 106.30 - 113.28: 14834 113.28 - 120.26: 9397 120.26 - 127.24: 11903 127.24 - 134.22: 241 Bond angle restraints: 37097 Sorted by residual: angle pdb=" C PHE A 55 " pdb=" N LEU A 56 " pdb=" CA LEU A 56 " ideal model delta sigma weight residual 122.65 133.35 -10.70 1.66e+00 3.63e-01 4.15e+01 angle pdb=" CA GLU B 281 " pdb=" CB GLU B 281 " pdb=" CG GLU B 281 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N LEU A 216 " pdb=" CA LEU A 216 " pdb=" C LEU A 216 " ideal model delta sigma weight residual 109.81 116.72 -6.91 2.21e+00 2.05e-01 9.78e+00 angle pdb=" CA ASP D 100 " pdb=" C ASP D 100 " pdb=" O ASP D 100 " ideal model delta sigma weight residual 121.68 118.10 3.58 1.18e+00 7.18e-01 9.19e+00 angle pdb=" N LEU B1141 " pdb=" CA LEU B1141 " pdb=" C LEU B1141 " ideal model delta sigma weight residual 114.62 111.22 3.40 1.14e+00 7.69e-01 8.90e+00 ... (remaining 37092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 15366 24.69 - 49.38: 1072 49.38 - 74.07: 170 74.07 - 98.76: 43 98.76 - 123.45: 32 Dihedral angle restraints: 16683 sinusoidal: 6957 harmonic: 9726 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 18.60 74.40 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 19.29 73.71 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 22.84 70.16 1 1.00e+01 1.00e-02 6.34e+01 ... (remaining 16680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3476 0.054 - 0.108: 686 0.108 - 0.162: 121 0.162 - 0.216: 2 0.216 - 0.270: 4 Chirality restraints: 4289 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C1 NAG A1207 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1207 " pdb=" O5 NAG A1207 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4286 not shown) Planarity restraints: 4801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO B 987 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 56 " 0.037 5.00e-02 4.00e+02 5.73e-02 5.24e+00 pdb=" N PRO C 57 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO C 987 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.032 5.00e-02 4.00e+02 ... (remaining 4798 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2121 2.74 - 3.28: 26505 3.28 - 3.82: 42594 3.82 - 4.36: 47430 4.36 - 4.90: 83850 Nonbonded interactions: 202500 Sorted by model distance: nonbonded pdb=" OG SER D 7 " pdb=" OG SER D 21 " model vdw 2.197 2.440 nonbonded pdb=" O SER C 975 " pdb=" OG SER C 975 " model vdw 2.198 2.440 nonbonded pdb=" O4 NAG C1201 " pdb=" O7 NAG C1201 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.220 2.440 nonbonded pdb=" O ALA C 352 " pdb=" OG SER C 399 " model vdw 2.220 2.440 ... (remaining 202495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 458 or resid 460 through 476 or resid 478 throu \ gh 675 or resid 690 through 827 or resid 852 through 1146 or resid 1203 through \ 1209)) selection = (chain 'B' and (resid 14 through 458 or resid 460 through 476 or resid 478 throu \ gh 617 or resid 641 through 827 or resid 852 through 940 or resid 944 through 11 \ 46 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 458 or resid 460 through 476 or resid 478 throu \ gh 675 or resid 690 through 827 or resid 852 through 1146 or resid 1203 through \ 1209)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 16.850 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 80.680 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 27253 Z= 0.236 Angle : 0.591 10.700 37097 Z= 0.301 Chirality : 0.045 0.270 4289 Planarity : 0.004 0.059 4771 Dihedral : 17.270 123.447 10360 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 0.51 % Allowed : 23.67 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3314 helix: 1.63 (0.22), residues: 619 sheet: 0.02 (0.22), residues: 587 loop : -1.65 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS B 49 PHE 0.015 0.001 PHE C 562 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 372 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 ARG cc_start: 0.7552 (tpt-90) cc_final: 0.7219 (ttt-90) REVERT: C 697 MET cc_start: 0.8407 (mtt) cc_final: 0.8057 (mtp) REVERT: C 808 ASP cc_start: 0.8424 (t0) cc_final: 0.8205 (t0) outliers start: 14 outliers final: 6 residues processed: 383 average time/residue: 0.3494 time to fit residues: 219.2718 Evaluate side-chains 364 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 358 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 259 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 300 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27253 Z= 0.256 Angle : 0.585 9.875 37097 Z= 0.288 Chirality : 0.046 0.317 4289 Planarity : 0.004 0.056 4771 Dihedral : 10.752 108.426 4377 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.72 % Favored : 93.19 % Rotamer: Outliers : 3.53 % Allowed : 21.75 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3314 helix: 1.93 (0.21), residues: 623 sheet: -0.03 (0.21), residues: 633 loop : -1.66 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.005 0.001 HIS B 49 PHE 0.018 0.001 PHE C 562 TYR 0.021 0.001 TYR B1067 ARG 0.006 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 371 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9141 (ptt) cc_final: 0.8853 (ptt) REVERT: A 979 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: A 1107 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.6886 (mpp-170) REVERT: B 542 ASN cc_start: 0.7992 (t0) cc_final: 0.7738 (t0) REVERT: B 1029 MET cc_start: 0.9256 (tpp) cc_final: 0.8934 (ttm) REVERT: C 275 PHE cc_start: 0.5471 (m-80) cc_final: 0.5257 (m-80) REVERT: C 353 TRP cc_start: -0.0381 (OUTLIER) cc_final: -0.0999 (m-90) REVERT: C 385 THR cc_start: 0.1973 (OUTLIER) cc_final: 0.1699 (m) REVERT: C 697 MET cc_start: 0.8335 (mtt) cc_final: 0.8025 (mtp) REVERT: C 808 ASP cc_start: 0.8317 (t0) cc_final: 0.8069 (t0) REVERT: C 996 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8850 (mp) REVERT: C 1029 MET cc_start: 0.9061 (tpp) cc_final: 0.8081 (ttm) outliers start: 102 outliers final: 57 residues processed: 437 average time/residue: 0.3551 time to fit residues: 254.7007 Evaluate side-chains 421 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 359 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 167 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 301 optimal weight: 1.9990 chunk 325 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 241 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27253 Z= 0.256 Angle : 0.562 8.285 37097 Z= 0.280 Chirality : 0.045 0.319 4289 Planarity : 0.004 0.057 4771 Dihedral : 8.838 101.675 4374 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.28 % Rotamer: Outliers : 3.91 % Allowed : 21.79 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3314 helix: 1.98 (0.21), residues: 631 sheet: -0.03 (0.21), residues: 635 loop : -1.66 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS B 49 PHE 0.020 0.001 PHE B 592 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 377 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9140 (ptt) cc_final: 0.8879 (ptt) REVERT: A 825 LYS cc_start: 0.8540 (tptp) cc_final: 0.8220 (tptp) REVERT: A 979 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: A 1107 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6898 (mpp-170) REVERT: B 542 ASN cc_start: 0.8026 (t0) cc_final: 0.7823 (t0) REVERT: C 298 GLU cc_start: 0.7140 (tt0) cc_final: 0.6830 (tt0) REVERT: C 353 TRP cc_start: -0.0301 (OUTLIER) cc_final: -0.0912 (m-90) REVERT: C 385 THR cc_start: 0.1956 (OUTLIER) cc_final: 0.1694 (m) REVERT: C 697 MET cc_start: 0.8321 (mtt) cc_final: 0.7956 (mtp) REVERT: C 808 ASP cc_start: 0.8386 (t0) cc_final: 0.8162 (t0) REVERT: C 811 LYS cc_start: 0.8725 (tppt) cc_final: 0.8217 (tptp) REVERT: C 1029 MET cc_start: 0.9078 (tpp) cc_final: 0.8038 (ttm) outliers start: 113 outliers final: 75 residues processed: 453 average time/residue: 0.3433 time to fit residues: 255.3624 Evaluate side-chains 444 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 365 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 297 optimal weight: 0.9990 chunk 226 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 302 optimal weight: 1.9990 chunk 319 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 286 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27253 Z= 0.280 Angle : 0.576 8.725 37097 Z= 0.287 Chirality : 0.045 0.325 4289 Planarity : 0.004 0.059 4771 Dihedral : 8.369 95.444 4373 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.29 % Favored : 92.62 % Rotamer: Outliers : 4.49 % Allowed : 21.41 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3314 helix: 2.00 (0.21), residues: 626 sheet: -0.04 (0.21), residues: 622 loop : -1.68 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.005 0.001 HIS B 49 PHE 0.020 0.001 PHE B 592 TYR 0.022 0.001 TYR A1067 ARG 0.007 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 377 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9169 (ptt) cc_final: 0.8931 (ptt) REVERT: A 825 LYS cc_start: 0.8566 (tptp) cc_final: 0.8243 (tptp) REVERT: A 979 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: A 1107 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6858 (mpp-170) REVERT: B 508 TYR cc_start: 0.7472 (m-80) cc_final: 0.7147 (m-80) REVERT: B 512 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.8806 (t) REVERT: B 542 ASN cc_start: 0.8058 (t0) cc_final: 0.7759 (t0) REVERT: B 1029 MET cc_start: 0.9285 (tpp) cc_final: 0.8967 (ttm) REVERT: C 353 TRP cc_start: -0.0244 (OUTLIER) cc_final: -0.0897 (m-90) REVERT: C 385 THR cc_start: 0.1724 (OUTLIER) cc_final: 0.1473 (m) REVERT: C 697 MET cc_start: 0.8455 (mtt) cc_final: 0.8021 (mtp) REVERT: C 808 ASP cc_start: 0.8344 (t0) cc_final: 0.8045 (t0) REVERT: C 904 TYR cc_start: 0.8065 (m-10) cc_final: 0.7751 (m-10) REVERT: C 996 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8860 (mp) REVERT: C 1029 MET cc_start: 0.9039 (tpp) cc_final: 0.8027 (ttm) REVERT: C 1139 ASP cc_start: 0.8278 (t0) cc_final: 0.7918 (t0) outliers start: 130 outliers final: 96 residues processed: 467 average time/residue: 0.3484 time to fit residues: 268.6957 Evaluate side-chains 467 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 365 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 273 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 163 optimal weight: 4.9990 chunk 287 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 49 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27253 Z= 0.241 Angle : 0.563 13.261 37097 Z= 0.278 Chirality : 0.045 0.331 4289 Planarity : 0.004 0.055 4771 Dihedral : 8.014 89.759 4373 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.62 % Favored : 93.25 % Rotamer: Outliers : 4.18 % Allowed : 22.17 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3314 helix: 2.06 (0.22), residues: 627 sheet: -0.02 (0.21), residues: 628 loop : -1.66 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS C1083 PHE 0.018 0.001 PHE C 275 TYR 0.021 0.001 TYR A1067 ARG 0.006 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 377 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.4188 (OUTLIER) cc_final: 0.3744 (m) REVERT: A 467 ASP cc_start: 0.8089 (t0) cc_final: 0.7685 (t70) REVERT: A 731 MET cc_start: 0.9184 (ptt) cc_final: 0.8763 (ptt) REVERT: A 825 LYS cc_start: 0.8481 (tptp) cc_final: 0.8137 (tptp) REVERT: A 979 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: A 1107 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6841 (mpp-170) REVERT: A 1139 ASP cc_start: 0.8454 (t0) cc_final: 0.8001 (t70) REVERT: B 206 LYS cc_start: 0.8471 (tptp) cc_final: 0.8245 (tptm) REVERT: B 508 TYR cc_start: 0.7430 (m-80) cc_final: 0.7092 (m-80) REVERT: B 512 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.8768 (t) REVERT: B 542 ASN cc_start: 0.8008 (t0) cc_final: 0.7580 (t0) REVERT: B 902 MET cc_start: 0.9188 (tpt) cc_final: 0.8631 (tpt) REVERT: C 353 TRP cc_start: -0.0132 (OUTLIER) cc_final: -0.0774 (m-90) REVERT: C 385 THR cc_start: 0.1788 (OUTLIER) cc_final: 0.1553 (m) REVERT: C 697 MET cc_start: 0.8474 (mtt) cc_final: 0.8041 (mtp) REVERT: C 1029 MET cc_start: 0.9011 (tpp) cc_final: 0.8146 (ttt) REVERT: C 1107 ARG cc_start: 0.7540 (ttm170) cc_final: 0.7145 (ttm170) outliers start: 121 outliers final: 96 residues processed: 458 average time/residue: 0.3372 time to fit residues: 257.0328 Evaluate side-chains 468 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 366 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 107 optimal weight: 0.0570 chunk 288 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 320 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 148 optimal weight: 0.0000 chunk 26 optimal weight: 0.0970 chunk 105 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 overall best weight: 0.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27253 Z= 0.148 Angle : 0.538 10.264 37097 Z= 0.264 Chirality : 0.044 0.331 4289 Planarity : 0.004 0.090 4771 Dihedral : 7.508 84.140 4371 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.66 % Favored : 94.22 % Rotamer: Outliers : 3.22 % Allowed : 23.26 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3314 helix: 2.14 (0.22), residues: 633 sheet: 0.10 (0.21), residues: 628 loop : -1.56 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 107 HIS 0.008 0.001 HIS C 655 PHE 0.015 0.001 PHE C 275 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 388 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 ASP cc_start: 0.8095 (t0) cc_final: 0.7733 (t70) REVERT: A 825 LYS cc_start: 0.8500 (tptp) cc_final: 0.8149 (tptp) REVERT: A 979 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: A 1107 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6804 (mpp-170) REVERT: A 1139 ASP cc_start: 0.8434 (t0) cc_final: 0.7970 (t70) REVERT: B 206 LYS cc_start: 0.8463 (tptp) cc_final: 0.8228 (tptm) REVERT: B 508 TYR cc_start: 0.7365 (m-80) cc_final: 0.7013 (m-80) REVERT: B 512 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.8691 (t) REVERT: B 541 PHE cc_start: 0.7933 (p90) cc_final: 0.7623 (p90) REVERT: B 542 ASN cc_start: 0.8031 (t0) cc_final: 0.7628 (t0) REVERT: B 660 TYR cc_start: 0.8558 (m-10) cc_final: 0.8357 (m-80) REVERT: B 902 MET cc_start: 0.9173 (tpt) cc_final: 0.8667 (tpt) REVERT: C 228 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.6013 (m-30) REVERT: C 385 THR cc_start: 0.1838 (OUTLIER) cc_final: 0.1567 (m) REVERT: C 777 ASN cc_start: 0.8580 (t0) cc_final: 0.8354 (t0) REVERT: C 1029 MET cc_start: 0.8990 (tpp) cc_final: 0.8009 (ttm) outliers start: 93 outliers final: 65 residues processed: 456 average time/residue: 0.3416 time to fit residues: 259.5391 Evaluate side-chains 442 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 372 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 308 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 182 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN C1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27253 Z= 0.252 Angle : 0.568 11.497 37097 Z= 0.281 Chirality : 0.046 0.324 4289 Planarity : 0.004 0.075 4771 Dihedral : 7.464 80.100 4371 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.93 % Favored : 92.95 % Rotamer: Outliers : 3.73 % Allowed : 22.75 % Favored : 73.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3314 helix: 2.15 (0.22), residues: 626 sheet: 0.04 (0.21), residues: 633 loop : -1.63 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.009 0.001 HIS C 655 PHE 0.016 0.001 PHE C 562 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 371 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.4087 (OUTLIER) cc_final: 0.3718 (m) REVERT: A 825 LYS cc_start: 0.8515 (tptp) cc_final: 0.8160 (tptp) REVERT: A 979 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: A 1107 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6775 (mpp-170) REVERT: A 1139 ASP cc_start: 0.8460 (t0) cc_final: 0.8013 (t70) REVERT: B 206 LYS cc_start: 0.8451 (tptp) cc_final: 0.8201 (tptm) REVERT: B 421 TYR cc_start: 0.8014 (m-10) cc_final: 0.7259 (m-10) REVERT: B 508 TYR cc_start: 0.7407 (m-80) cc_final: 0.7054 (m-80) REVERT: B 512 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.8755 (t) REVERT: B 541 PHE cc_start: 0.7933 (p90) cc_final: 0.7636 (p90) REVERT: B 542 ASN cc_start: 0.8054 (t0) cc_final: 0.7613 (t0) REVERT: B 1050 MET cc_start: 0.9118 (ptm) cc_final: 0.8912 (ptp) REVERT: C 49 HIS cc_start: 0.7884 (t70) cc_final: 0.7279 (t-170) REVERT: C 353 TRP cc_start: -0.0173 (OUTLIER) cc_final: -0.0790 (m-90) REVERT: C 756 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7958 (t80) REVERT: C 777 ASN cc_start: 0.8735 (t0) cc_final: 0.8375 (t0) REVERT: C 996 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8843 (mp) REVERT: C 1029 MET cc_start: 0.9042 (tpp) cc_final: 0.8026 (ttm) REVERT: C 1107 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7186 (ttm170) outliers start: 108 outliers final: 90 residues processed: 451 average time/residue: 0.3410 time to fit residues: 255.9779 Evaluate side-chains 465 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 368 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 157 optimal weight: 0.0060 chunk 29 optimal weight: 0.3980 chunk 250 optimal weight: 0.4980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27253 Z= 0.197 Angle : 0.557 9.493 37097 Z= 0.274 Chirality : 0.045 0.413 4289 Planarity : 0.004 0.065 4771 Dihedral : 7.281 74.506 4371 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.35 % Favored : 93.53 % Rotamer: Outliers : 3.73 % Allowed : 22.92 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3314 helix: 2.19 (0.22), residues: 626 sheet: 0.22 (0.22), residues: 600 loop : -1.60 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.010 0.001 HIS C 655 PHE 0.014 0.001 PHE C 562 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 367 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 825 LYS cc_start: 0.8514 (tptp) cc_final: 0.8166 (tptp) REVERT: A 979 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: A 1107 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6824 (mpp-170) REVERT: B 153 MET cc_start: 0.2744 (pmm) cc_final: 0.2519 (pmm) REVERT: B 206 LYS cc_start: 0.8456 (tptp) cc_final: 0.8204 (tptm) REVERT: B 508 TYR cc_start: 0.7374 (m-80) cc_final: 0.7028 (m-80) REVERT: B 512 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.8726 (t) REVERT: B 541 PHE cc_start: 0.7949 (p90) cc_final: 0.7706 (p90) REVERT: B 542 ASN cc_start: 0.8085 (t0) cc_final: 0.7632 (t0) REVERT: C 49 HIS cc_start: 0.7902 (t70) cc_final: 0.7306 (t-170) REVERT: C 353 TRP cc_start: -0.0190 (OUTLIER) cc_final: -0.0790 (m-90) REVERT: C 756 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.7898 (t80) REVERT: C 777 ASN cc_start: 0.8688 (t0) cc_final: 0.8346 (t0) REVERT: C 1029 MET cc_start: 0.9005 (tpp) cc_final: 0.8025 (ttm) outliers start: 108 outliers final: 90 residues processed: 446 average time/residue: 0.3330 time to fit residues: 247.3794 Evaluate side-chains 457 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 362 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 290 optimal weight: 0.1980 chunk 305 optimal weight: 0.6980 chunk 278 optimal weight: 0.9980 chunk 297 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 233 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 296 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27253 Z= 0.201 Angle : 0.551 8.978 37097 Z= 0.272 Chirality : 0.045 0.335 4289 Planarity : 0.004 0.060 4771 Dihedral : 6.930 64.821 4371 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.23 % Favored : 93.65 % Rotamer: Outliers : 3.49 % Allowed : 23.12 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3314 helix: 2.21 (0.22), residues: 626 sheet: 0.13 (0.21), residues: 615 loop : -1.58 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.010 0.001 HIS C 655 PHE 0.015 0.001 PHE C 562 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 377 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 825 LYS cc_start: 0.8526 (tptp) cc_final: 0.8168 (tptp) REVERT: A 979 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: A 1107 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6775 (mpp-170) REVERT: B 153 MET cc_start: 0.2843 (pmm) cc_final: 0.2633 (pmm) REVERT: B 206 LYS cc_start: 0.8464 (tptp) cc_final: 0.8208 (tptm) REVERT: B 508 TYR cc_start: 0.7357 (m-80) cc_final: 0.7014 (m-80) REVERT: B 512 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.8719 (t) REVERT: B 541 PHE cc_start: 0.7975 (p90) cc_final: 0.7746 (p90) REVERT: B 542 ASN cc_start: 0.8078 (t0) cc_final: 0.7603 (t0) REVERT: B 902 MET cc_start: 0.9206 (tpt) cc_final: 0.8596 (tpt) REVERT: C 49 HIS cc_start: 0.7888 (t70) cc_final: 0.7291 (t-170) REVERT: C 228 ASP cc_start: 0.6729 (m-30) cc_final: 0.6251 (m-30) REVERT: C 353 TRP cc_start: -0.0189 (OUTLIER) cc_final: -0.0783 (m-90) REVERT: C 756 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7904 (t80) REVERT: C 777 ASN cc_start: 0.8678 (t0) cc_final: 0.8334 (t0) REVERT: C 808 ASP cc_start: 0.8372 (t0) cc_final: 0.8115 (t0) REVERT: C 1029 MET cc_start: 0.9012 (tpp) cc_final: 0.8053 (ttm) REVERT: C 1139 ASP cc_start: 0.8291 (t0) cc_final: 0.7946 (t0) outliers start: 101 outliers final: 87 residues processed: 446 average time/residue: 0.3381 time to fit residues: 252.4276 Evaluate side-chains 464 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 372 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 195 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 329 optimal weight: 0.9980 chunk 303 optimal weight: 0.0020 chunk 262 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 161 optimal weight: 0.4980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 856 ASN C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27253 Z= 0.175 Angle : 0.547 8.850 37097 Z= 0.269 Chirality : 0.044 0.324 4289 Planarity : 0.004 0.059 4771 Dihedral : 6.658 57.660 4371 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.05 % Favored : 93.83 % Rotamer: Outliers : 3.15 % Allowed : 23.57 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3314 helix: 2.17 (0.22), residues: 632 sheet: 0.11 (0.21), residues: 627 loop : -1.55 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.010 0.001 HIS C 655 PHE 0.013 0.001 PHE C 562 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 380 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 825 LYS cc_start: 0.8533 (tptp) cc_final: 0.8200 (tptp) REVERT: A 979 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: A 1107 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6775 (mpp-170) REVERT: B 153 MET cc_start: 0.2864 (pmm) cc_final: 0.2656 (pmm) REVERT: B 206 LYS cc_start: 0.8444 (tptp) cc_final: 0.8074 (tptm) REVERT: B 224 GLU cc_start: 0.6994 (mp0) cc_final: 0.6269 (mp0) REVERT: B 508 TYR cc_start: 0.7338 (m-80) cc_final: 0.6970 (m-80) REVERT: B 512 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.8700 (t) REVERT: B 542 ASN cc_start: 0.8008 (t0) cc_final: 0.7562 (t0) REVERT: B 902 MET cc_start: 0.9226 (tpt) cc_final: 0.8671 (tpt) REVERT: B 954 GLN cc_start: 0.8597 (tt0) cc_final: 0.8308 (mt0) REVERT: C 49 HIS cc_start: 0.7949 (t70) cc_final: 0.7319 (t-170) REVERT: C 228 ASP cc_start: 0.6592 (m-30) cc_final: 0.6086 (m-30) REVERT: C 353 TRP cc_start: -0.0121 (OUTLIER) cc_final: -0.0697 (m-90) REVERT: C 756 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.7945 (t80) REVERT: C 777 ASN cc_start: 0.8614 (t0) cc_final: 0.8323 (t0) REVERT: C 808 ASP cc_start: 0.8400 (t0) cc_final: 0.8148 (t0) REVERT: C 1029 MET cc_start: 0.8996 (tpp) cc_final: 0.7991 (ttm) REVERT: C 1139 ASP cc_start: 0.8330 (t0) cc_final: 0.7971 (t0) outliers start: 91 outliers final: 81 residues processed: 441 average time/residue: 0.3408 time to fit residues: 249.7988 Evaluate side-chains 465 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 379 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 208 optimal weight: 0.5980 chunk 279 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 263 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 270 optimal weight: 0.1980 chunk 33 optimal weight: 0.1980 chunk 48 optimal weight: 0.0040 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.240863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.163374 restraints weight = 69058.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.160943 restraints weight = 30300.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.162476 restraints weight = 21864.379| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27253 Z= 0.157 Angle : 0.536 9.291 37097 Z= 0.263 Chirality : 0.044 0.332 4289 Planarity : 0.004 0.056 4771 Dihedral : 6.255 57.971 4371 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.78 % Favored : 94.10 % Rotamer: Outliers : 2.77 % Allowed : 23.98 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3314 helix: 2.30 (0.22), residues: 626 sheet: 0.18 (0.22), residues: 620 loop : -1.53 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.010 0.001 HIS C 655 PHE 0.012 0.001 PHE B 392 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5931.79 seconds wall clock time: 108 minutes 39.37 seconds (6519.37 seconds total)